+ /** DOCUMENT ME!! */\r
+ public static Desktop instance;\r
+ public static JDesktopPane desktop;\r
+ static int openFrameCount = 0;\r
+ static final int xOffset = 30;\r
+ static final int yOffset = 30;\r
+ public static jalview.ws.Discoverer discoverer;\r
+\r
+ public static Object [] jalviewClipboard;\r
+\r
+ static int fileLoadingCount= 0;\r
+\r
+ /**\r
+ * Creates a new Desktop object.\r
+ */\r
+ public Desktop()\r
+ {\r
+ instance = this;\r
+\r
+ Image image = null;\r
+\r
+ try\r
+ {\r
+ java.net.URL url = getClass().getResource("/images/logo.gif");\r
+\r
+ if (url != null)\r
+ {\r
+ image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+\r
+ MediaTracker mt = new MediaTracker(this);\r
+ mt.addImage(image, 0);\r
+ mt.waitForID(0);\r
+ setIconImage(image);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));\r
+ setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
+ desktop = new JDesktopPane();\r
+ desktop.setBackground(Color.white);\r
+ getContentPane().setLayout(new BorderLayout());\r
+ getContentPane().add(desktop, BorderLayout.CENTER);\r
+ desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
+\r
+ // This line prevents Windows Look&Feel resizing all new windows to maximum\r
+ // if previous window was maximised\r
+ desktop.setDesktopManager(new DefaultDesktopManager());\r
+\r
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
+ String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
+ String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
+ String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
+ String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
+\r
+ if ((x != null) && (y != null) && (width != null) && (height != null))\r
+ {\r
+ setBounds(Integer.parseInt(x), Integer.parseInt(y),\r
+ Integer.parseInt(width), Integer.parseInt(height));\r
+ }\r
+ else\r
+ {\r
+ setBounds((int) (screenSize.width - 900) / 2,\r
+ (int) (screenSize.height - 650) / 2, 900, 650);\r
+ }\r
+\r
+ this.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ quit();\r
+ }\r
+ });\r
+\r
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
+\r
+ /////////Add a splashscreen on startup\r
+ /////////Add a splashscreen on startup\r
+ JInternalFrame frame = new JInternalFrame();\r
+\r
+ SplashScreen splash = new SplashScreen(frame, image);\r
+ frame.setContentPane(splash);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ frame.setLocation((int) ((getWidth() - 750) / 2),\r
+ (int) ((getHeight() - 160) / 2));\r
+\r
+ addInternalFrame(frame, "", 750, 160, false);\r
+\r
+ discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param frame DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ * @param w DOCUMENT ME!\r
+ * @param h DOCUMENT ME!\r
+ */\r
+ public static synchronized void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h)\r
+ {\r
+ addInternalFrame(frame, title, w, h, true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param frame DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ * @param w DOCUMENT ME!\r
+ * @param h DOCUMENT ME!\r
+ * @param resizable DOCUMENT ME!\r
+ */\r
+ public static synchronized void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h, boolean resizable)\r
+ {\r
+\r
+ frame.setTitle(title);\r
+ if(frame.getWidth()<1 || frame.getHeight()<1)\r
+ {\r
+ frame.setSize(w, h);\r
+ }\r
+ // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN\r
+ // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN\r
+ // IF JALVIEW IS RUNNING HEADLESS\r
+ /////////////////////////////////////////////////\r
+ if (System.getProperty("java.awt.headless") != null\r
+ && System.getProperty("java.awt.headless").equals("true"))\r
+ {\r
+ return;\r
+ }\r
+\r
+\r
+ openFrameCount++;\r
+\r
+ frame.setVisible(true);\r
+ frame.setClosable(true);\r
+ frame.setResizable(resizable);\r
+ frame.setMaximizable(resizable);\r
+ frame.setIconifiable(resizable);\r
+ frame.setFrameIcon(null);\r
+\r
+ if (frame.getX()<1 && frame.getY()<1)\r
+ {\r
+ frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);\r
+ }\r
+\r
+ final JMenuItem menuItem = new JMenuItem(title);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameActivated(javax.swing.event.\r
+ InternalFrameEvent evt)\r
+ {\r
+ JInternalFrame itf = desktop.getSelectedFrame();\r
+ if (itf != null)\r
+ itf.requestFocus();\r
+\r
+ }\r
+\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ openFrameCount--;\r
+ windowMenu.remove(menuItem);\r
+ JInternalFrame itf = desktop.getSelectedFrame();\r
+ if (itf != null)\r
+ itf.requestFocus();\r
+ }\r
+ ;\r
+ });\r
+\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ frame.setSelected(true);\r
+ frame.setIcon(false);\r
+ }\r
+ catch (java.beans.PropertyVetoException ex)\r
+ {\r
+\r
+ }\r
+ }\r
+ });\r
+\r
+ windowMenu.add(menuItem);\r
+\r
+ desktop.add(frame);\r
+ frame.toFront();\r
+ try{\r
+ frame.setSelected(true);\r
+ frame.requestFocus();\r
+ }catch(java.beans.PropertyVetoException ve)\r
+ {}\r
+ }\r
+\r
+ public void lostOwnership(Clipboard clipboard, Transferable contents)\r
+ {\r
+ Desktop.jalviewClipboard = null;\r
+ }\r
+\r
+ public void dragEnter(DropTargetDragEvent evt)\r
+ {}\r
+\r
+ public void dragExit(DropTargetEvent evt)\r
+ {}\r
+\r
+ public void dragOver(DropTargetDragEvent evt)\r
+ {}\r
+\r
+ public void dropActionChanged(DropTargetDragEvent evt)\r
+ {}\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void drop(DropTargetDropEvent evt)\r
+ {\r
+ Transferable t = evt.getTransferable();\r
+ java.util.List files = null;\r
+\r
+ try\r
+ {\r
+ DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");\r
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ {\r
+ //Works on Windows and MacOSX\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
+ }\r
+ else if (t.isDataFlavorSupported(uriListFlavor))\r
+ {\r
+ // This is used by Unix drag system\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ String data = (String) t.getTransferData(uriListFlavor);\r
+ files = new java.util.ArrayList(1);\r
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(\r
+ data,\r
+ "\r\n");\r
+ st.hasMoreTokens(); )\r
+ {\r
+ String s = st.nextToken();\r
+ if (s.startsWith("#"))\r
+ {\r
+ // the line is a comment (as per the RFC 2483)\r
+ continue;\r
+ }\r
+\r
+ java.net.URI uri = new java.net.URI(s);\r
+ java.io.File file = new java.io.File(uri);\r
+ files.add(file);\r
+ }\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ if (files != null)\r
+ {\r
+ try\r
+ {\r
+ for (int i = 0; i < files.size(); i++)\r
+ {\r
+ String file = files.get(i).toString();\r
+ String protocol = FormatAdapter.FILE;\r
+ String format = null;\r
+\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ format = "Jalview";\r
+\r
+ }\r
+ else\r
+ {\r
+ format = new IdentifyFile().Identify(file,\r
+ protocol);\r
+ }\r
+\r
+\r
+ new FileLoader().LoadFile(file, protocol, format);\r
+\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Open local file");\r
+ chooser.setToolTipText("Open");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ String format = null;\r
+ if (chooser.getSelectedFormat().equals("Jalview"))\r
+ {\r
+ format = "Jalview";\r
+ }\r
+ else\r
+ {\r
+ format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);\r
+ }\r
+\r
+ if (viewport != null)\r
+ new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);\r
+ else\r
+ new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);\r
+ }\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport)\r
+ {\r
+ // This construct allows us to have a wider textfield\r
+ // for viewing\r
+ JLabel label = new JLabel("Enter URL of Input File");\r
+ final JComboBox history = new JComboBox();\r
+\r
+ JPanel panel = new JPanel(new GridLayout(2,1));\r
+ panel.add(label);\r
+ panel.add(history);\r
+ history.setPreferredSize(new Dimension(400,20));\r
+ history.setEditable(true);\r
+ history.addItem("http://www.");\r
+\r
+ String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");\r
+\r
+ StringTokenizer st;\r
+\r
+ if (historyItems != null)\r